Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2630 to 2679 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
658 Ranked aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 229.072 216.576 1.0577
Squared similar to trna synthetase class ii. [refseq;acc:nm_152268] 22293.8 26242.6 1.17713
Rooted eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 52.7523 56.8686 1.07803
659 Measured shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 6089.21 6835.34 1.12253
Ranked hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] 229.072 216.576 1.0577
Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 24614 28973.4 1.17711
Rooted 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 51.7081 47.9816 1.07767
660 Measured u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 5575.18 6254.85 1.12191
Ranked actin binding lim protein 2. [refseq;acc:nm_032432] 229.072 216.576 1.0577
Squared nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 33024.9 38867.8 1.17692
Rooted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 133.216 123.627 1.07756
661 Measured step ii splicing factor slu7. [refseq;acc:nm_006425] 5575.18 6254.85 1.12191
Ranked hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 229.072 216.576 1.0577
Squared delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 22223.1 26152.4 1.17681
Rooted nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 68.8243 74.1496 1.07738
662 Measured partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 6374.65 7145.59 1.12094
Ranked synapsin ii. [swissprot;acc:q92777] 229.072 216.576 1.0577
Squared ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 23947.4 28163.7 1.17607
Rooted nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 68.8237 74.1484 1.07737
663 Measured tubby protein homolog. [swissprot;acc:p50607] 6374.65 7145.59 1.12094
Ranked mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 229.072 216.576 1.0577
Squared acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
Rooted nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 68.8197 74.1413 1.07733
664 Measured protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 6374.65 7145.59 1.12094
Ranked peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 229.072 216.576 1.0577
Squared ubiquitin-like protein smt3a. [swissprot;acc:p55854] 23948 28164.1 1.17605
Rooted neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 51.6042 55.574 1.07693
665 Measured numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 6374.65 7145.59 1.12094
Ranked hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 229.072 216.576 1.0577
Squared u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 18960.3 22298 1.17604
Rooted rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] 51.6042 55.574 1.07693
666 Measured tbc1 domain family member 5. [swissprot;acc:q92609] 6374.65 7145.59 1.12094
Ranked transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 229.072 216.576 1.0577
Squared glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 29224 34362.1 1.17582
Rooted down-regulated in metastasis. [refseq;acc:nm_014503] 51.6042 55.574 1.07693
667 Measured tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 6374.65 7145.59 1.12094
Ranked delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 229.072 216.576 1.0577
Squared proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] 29224 34362.1 1.17582
Rooted ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 51.2483 47.5889 1.0769
668 Measured vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] 6374.65 7145.59 1.12094
Ranked actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 229.072 216.576 1.0577
Squared isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 23969.3 28175.3 1.17547
Rooted acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 95.4476 102.785 1.07687
669 Measured numb-like protein (numb-r). [swissprot;acc:q9y6r0] 6374.65 7145.59 1.12094
Ranked synapsin i (brain protein 4.1). [swissprot;acc:p17600] 229.072 216.576 1.0577
Squared u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 18548.7 21798.2 1.17519
Rooted hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 79.931 86.0693 1.07679
670 Measured tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 6374.65 7145.59 1.12094
Ranked autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 1.05694
Squared dok-like protein. [refseq;acc:nm_024872] 28911 33971.3 1.17503

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/